Dear FreeSurfer experts,
I am trying to run mris_preproc after caching my data. As command lines, I am
typing:
mris_preproc --fsgd file.fsgd \
--cache-in thickness.fwhm10.fsaverage \
--target fsaverage --hemi lh \
--out lh.allpatients.thickness10.mgh
Everytime I am trying to run these commands,
Could it be that the mris_preproc and the mri_glmfit file are missing in my
freesurfer package? If so, can anybody send them to me?
Thank you very much,
Julia
Von: Richter, Julia
Gesendet: Dienstag, 5. Juni 2012 10:11
Bis: freesurfer@nmr.mgh.harvard.edu
Betreff:
Dear Doug,
I am having a partial field of view and a full brain scan. How can I integrate
the results in the preproc-sess sequence in order to complete the preprocessing
correctly?
Cheers pfannmoe
On Mon, 04 Jun 2012 11:42:32 -0400
Douglas N Greve wrote:
> You can try running register-sess
Hi Julia
that seems unlikely. What happens when you type:
ls $FREESURFER_HOME/bin/mris_preproc
cheers
Bruce
On Tue, 5 Jun 2012,
Richter, Julia wrote:
> Could it be that the mris_preproc and the mri_glmfit file are missing in my
> freesurfer package? If so, can anybody send them to me?
>
> Tha
Dear Freesurfer experts,
I have performed a VBM analysis with SPM, using some VOIs. Now I would like
to compare the volumetric results obtained with SPM with those of cortical
thickness obtained with Freesurfer in the same VOIs (approximately).
For this purpose, I would like to transform the MNI
after typing your command in my terminal window, it appears:
/usr/local/freesurfer/bin/mris_preproc
Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 5. Juni 2012 15:05
Bis: Richter, Julia
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [F
okay, how about:
which mris_preproc
and just
mris_preproc
On Tue, 5 Jun 2012, Richter, Julia wrote:
> after typing your command in my terminal window, it appears:
>
> /usr/local/freesurfer/bin/mris_preproc
>
> Von: Bruce Fischl [fis...@nmr.mgh.harvard.e
nothing happens when typing "which mris_prepoc", command not found when typing
only "mris_preproc"
Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 5. Juni 2012 15:25
Bis: Richter, Julia
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: AW:
so your path must be wrong then. Are you sourcing
$FREESURFER_HOME/FreeSurferEnv.csh? That is, in your .login or .cshrc or
whatever gets run at startup do you do:
source $FREESURFER_HOME/FreeSurferEnv.csh
try running that at the command line and see if it finds mris_preproc
afterwards.
cheers
Hello,
I was hoping somebody could help me out. I am trying to create a label file for
the aparc+aseg file. All I'm wanting is the pixel value and the label. I know
there is the FreeSurferColorLUT.txt file which contains this information, but
looking at this file I can tell that all of these la
Hi Cyrus,
You can run the following script:
compute_label_volumes.csh
It will list all the labels that are in your segmentation file (and also
tell you the number of voxels colored by this label and th etotal volume).
Lilla
On Tue, 5 Jun 2012, Sarosh, Cyrus wrote:
Hello,
I was hopin
Hi,
what would you consider a small sample? I have one sample of 40 participants
(20 patients, 20 controls) for that I thought it would be best to use the
fsaverage and then maybe display it on my own subjects average.
The other study consists of roughly 140 participants (1/3 are healthy con
You can't do directly from preproc-sess, but you can do it from
register-sess if you have an additional whole brain acquisition in the
same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc)
as long as it is whole brain. If your anatomical was acquired in the
same session, then
Hi Tony, you can use bbregister to create the registration file. You
might also look at the multi-modal tutorial on our wiki as this goes
over the steps that you will need to get and apply the registration.
For the 2nd question, you can use mris_anatomical_stats.
dou
The final recon process, autorecon3 - uses "ASegStatsLUT.txt" by default to
segment certain subcortical structures listed within this textfile.
On the otherhand, FreeSurferColorLUT.txt has labels for more subregions,
including the substancia nigra which is a region of interest for a particular
not currently, sorry
On Wed, 6 Jun 2012, Zohra Ahmadzai wrote:
>
> The final recon process, autorecon3 - uses "ASegStatsLUT.txt" by default to
> segment certain subcortical structures listed within this textfile.
>
> On the otherhand, FreeSurferColorLUT.txt has labels for more subregions,
> incl
Hello,
With FreeSurfer v4.5, I have three functionally localized surface labels
(A.label, B.label, C.label), and converted this label to volume by using
mri_label2vol with --proj. I now have three volume labels, A.mgz, B.mgz, and
C.mgz.
Because these three labels are adjacent to each other, [
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